refactor: migrate from KuzuDB to LadybugDB v0.15

.github/workflows/ci-integration.yml

@@ -12,29 +12,29 @@ on:
 jobs:
   # ── Integration test matrix ─────────────────────────────────────────
   # Each test-group runs on a SEPARATE runner per OS, giving full process
-  # isolation for the KuzuDB native C++ addon.
+  # isolation for the LadybugDB native C++ addon.
   # 3 OS x 4 groups = 12 parallel jobs.
   #
   # Groups:
-  #   kuzu-db    — 7 files using withTestKuzuDB / kuzu-adapter (native addon)
+  #   lbug-db    — 7 files using withTestLbugDB / lbug-adapter (native addon)
   #                Each file runs as its own `vitest run` invocation for full
-  #                process isolation. KuzuDB's native N-API addon registers
+  #                process isolation. LadybugDB's native N-API addon registers
   #                persistent handles that prevent fork workers from exiting
   #                on Linux, and its C++ destructors segfault during
   #                process.exit(). Running each file in its own process lets
   #                the OS reclaim all resources cleanly.
-  #   pipeline   — 13 files: ingestion pipeline + csv + 10 resolver tests
-  #   e2e        — 2 files: child-process only (spawnSync), no in-process kuzu
-  #   standalone — 4 files: pure logic, no kuzu, no child processes
+  #   pipeline   — 12 files: ingestion pipeline + csv + 9 resolver tests
+  #   e2e        — 2 files: child-process only (spawnSync), no in-process lbug
+  #   standalone — 4 files: pure logic, no lbug, no child processes
   test-matrix:
     name: integration (${{ matrix.os }} / ${{ matrix.test-group }})
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        test-group: [kuzu-db, pipeline, e2e, standalone]
+        test-group: [lbug-db, pipeline, e2e, standalone]
         include:
-          - test-group: kuzu-db
+          - test-group: lbug-db
             # Marker — actual files are listed in the run step below
             test-glob: ''
           - test-group: pipeline
@@ -72,18 +72,18 @@ jobs:
         with:
           build: 'true'
 
-      # kuzu-db: run each file in its own vitest process for full isolation.
-      # KuzuDB's native addon hangs fork workers on Linux — process isolation
+      # lbug-db: run each file in its own vitest process for full isolation.
+      # LadybugDB's native addon hangs fork workers on Linux — process isolation
       # is the only reliable fix boundary.
-      - name: Run integration tests — kuzu-db (process-isolated)
-        if: matrix.test-group == 'kuzu-db'
+      - name: Run integration tests — lbug-db (process-isolated)
+        if: matrix.test-group == 'lbug-db'
         working-directory: gitnexus
         shell: bash
         run: |
           set -e
           files=(
-            test/integration/kuzu-core-adapter.test.ts
-            test/integration/kuzu-pool.test.ts
+            test/integration/lbug-core-adapter.test.ts
+            test/integration/lbug-pool.test.ts
             test/integration/local-backend.test.ts
             test/integration/local-backend-calltool.test.ts
             test/integration/search-core.test.ts
@@ -101,19 +101,19 @@ jobs:
           done
           exit $exit_code
 
-      # Non-kuzu groups: run all files in a single vitest invocation
+      # Non-lbug groups: run all files in a single vitest invocation
       - name: Run integration tests — ${{ matrix.test-group }}
-        if: matrix.test-group != 'kuzu-db'
+        if: matrix.test-group != 'lbug-db'
         shell: bash
         env:
           TEST_GLOB: ${{ matrix.test-glob }}
         run: npx vitest run --reporter=verbose $TEST_GLOB
         working-directory: gitnexus
 
   # ── Coverage collection (ubuntu only) ─────────────────────────────────
-  # Runs non-kuzu integration tests with coverage enabled so the PR report
+  # Runs non-lbug integration tests with coverage enabled so the PR report
   # can merge integration + unit coverage for a combined view.
-  # kuzu-db tests are excluded because each file must run in its own vitest
+  # lbug-db tests are excluded because each file must run in its own vitest
   # process (native addon isolation) which prevents single-run coverage merge.
   coverage:
     name: integration (ubuntu / coverage)

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 All notable changes to GitNexus will be documented in this file.
 
+## [Unreleased]
+
+### Changed
+- Migrated from KuzuDB to LadybugDB v0.15 (`@ladybugdb/core`, `@ladybugdb/wasm-core`)
+- Renamed all internal paths from `kuzu` to `lbug` (storage: `.gitnexus/kuzu` → `.gitnexus/lbug`)
+- Added automatic cleanup of stale KuzuDB index files
+- LadybugDB v0.15 requires explicit VECTOR extension loading for semantic search
+
 ## [1.4.0] - 2026-03-13
 
 ### Added

README.md

@@ -51,7 +51,7 @@ https://github.com/user-attachments/assets/172685ba-8e54-4ea7-9ad1-e31a3398da72
 | **For**     | Daily development with Cursor, Claude Code, Windsurf, OpenCode | Quick exploration, demos, one-off analysis                   |
 | **Scale**   | Full repos, any size                                           | Limited by browser memory (~5k files), or unlimited via backend mode |
 | **Install** | `npm install -g gitnexus`                                    | No install —[gitnexus.vercel.app](https://gitnexus.vercel.app) |
-| **Storage** | KuzuDB native (fast, persistent)                               | KuzuDB WASM (in-memory, per session)                         |
+| **Storage** | LadybugDB native (fast, persistent)                               | LadybugDB WASM (in-memory, per session)                         |
 | **Parsing** | Tree-sitter native bindings                                    | Tree-sitter WASM                                             |
 | **Privacy** | Everything local, no network                                   | Everything in-browser, no server                             |
 
@@ -224,8 +224,8 @@ flowchart TD
         Server["server.ts"]
         Backend["LocalBackend"]
         Pool["Connection Pool"]
-        ConnA["KuzuDB conn A"]
-        ConnB["KuzuDB conn B"]
+        ConnA["LadybugDB conn A"]
+        ConnB["LadybugDB conn B"]
     end
 
     Setup -->|"writes global MCP config"| CursorConfig["~/.cursor/mcp.json"]
@@ -242,7 +242,7 @@ flowchart TD
     ConnB -->|"queries"| RepoB
 ```
 
-**How it works:** Each `gitnexus analyze` stores the index in `.gitnexus/` inside the repo (portable, gitignored) and registers a pointer in `~/.gitnexus/registry.json`. When an AI agent starts, the MCP server reads the registry and can serve any indexed repo. KuzuDB connections are opened lazily on first query and evicted after 5 minutes of inactivity (max 5 concurrent). If only one repo is indexed, the `repo` parameter is optional on all tools — agents don't need to change anything.
+**How it works:** Each `gitnexus analyze` stores the index in `.gitnexus/` inside the repo (portable, gitignored) and registers a pointer in `~/.gitnexus/registry.json`. When an AI agent starts, the MCP server reads the registry and can serve any indexed repo. LadybugDB connections are opened lazily on first query and evicted after 5 minutes of inactivity (max 5 concurrent). If only one repo is indexed, the `repo` parameter is optional on all tools — agents don't need to change anything.
 
 ---
 
@@ -263,7 +263,7 @@ npm install
 npm run dev
 ```
 
-The web UI uses the same indexing pipeline as the CLI but runs entirely in WebAssembly (Tree-sitter WASM, KuzuDB WASM, in-browser embeddings). It's great for quick exploration but limited by browser memory for larger repos.
+The web UI uses the same indexing pipeline as the CLI but runs entirely in WebAssembly (Tree-sitter WASM, LadybugDB WASM, in-browser embeddings). It's great for quick exploration but limited by browser memory for larger repos.
 
 **Local Backend Mode:** Run `gitnexus serve` and open the web UI locally — it auto-detects the server and shows all your indexed repos, with full AI chat support. No need to re-upload or re-index. The agent's tools (Cypher queries, search, code navigation) route through the backend HTTP API automatically.
 
@@ -482,7 +482,7 @@ The wiki generator reads the indexed graph structure, groups files into modules
 | ------------------------- | ------------------------------------- | --------------------------------------- |
 | **Runtime**         | Node.js (native)                      | Browser (WASM)                          |
 | **Parsing**         | Tree-sitter native bindings           | Tree-sitter WASM                        |
-| **Database**        | KuzuDB native                         | KuzuDB WASM                             |
+| **Database**        | LadybugDB native                         | LadybugDB WASM                             |
 | **Embeddings**      | HuggingFace transformers.js (GPU/CPU) | transformers.js (WebGPU/WASM)           |
 | **Search**          | BM25 + semantic + RRF                 | BM25 + semantic + RRF                   |
 | **Agent Interface** | MCP (stdio)                           | LangChain ReAct agent                   |
@@ -523,7 +523,7 @@ The wiki generator reads the indexed graph structure, groups files into modules
 ## Acknowledgments
 
 - [Tree-sitter](https://tree-sitter.github.io/) — AST parsing
-- [KuzuDB](https://kuzudb.com/) — Embedded graph database with vector support
+- [LadybugDB](https://ladybugdb.com/) — Embedded graph database with vector support (formerly KuzuDB)
 - [Sigma.js](https://www.sigmajs.org/) — WebGL graph rendering
 - [transformers.js](https://huggingface.co/docs/transformers.js) — Browser ML
 - [Graphology](https://graphology.github.io/) — Graph data structures

eval/README.md

@@ -148,7 +148,7 @@ Each mode has a `system_{mode}.jinja` + `instance_{mode}.jinja` pair. The agent
 
 1. Docker container starts with SWE-bench instance (repo at specific commit)
 2. **GitNexus setup**: Node.js + gitnexus installed, `gitnexus analyze` runs (or restores from cache)
-3. **Eval-server starts**: `gitnexus eval-server` daemon (persistent HTTP server, keeps KuzuDB warm)
+3. **Eval-server starts**: `gitnexus eval-server` daemon (persistent HTTP server, keeps LadybugDB warm)
 4. **Standalone tool scripts installed** in `/usr/local/bin/` — works with `subprocess.run` (no `.bashrc` needed)
 5. Agent runs with the configured model + system prompt + GitNexus tools
 6. Agent's patch is extracted as a git diff
@@ -167,7 +167,7 @@ Each tool script in `/usr/local/bin/` is standalone — no sourcing, no env inhe
 ### Eval-server
 
 The eval-server is a lightweight HTTP daemon that:
-- Keeps KuzuDB warm in memory (no cold start per tool call)
+- Keeps LadybugDB warm in memory (no cold start per tool call)
 - Returns LLM-friendly text (not raw JSON — saves tokens)
 - Includes next-step hints to guide tool chaining (query → context → impact → fix)
 - Auto-shuts down after idle timeout

gitnexus-claude-plugin/hooks/gitnexus-hook.js

@@ -160,7 +160,7 @@ function handlePreToolUse(input) {
  * PostToolUse handler — detect index staleness after git mutations.
  *
  * Instead of spawning a full `gitnexus analyze` synchronously (which blocks
- * the agent for up to 120s and risks KuzuDB corruption on timeout), we do a
+ * the agent for up to 120s and risks LadybugDB corruption on timeout), we do a
  * lightweight staleness check: compare `git rev-parse HEAD` against the
  * lastCommit stored in `.gitnexus/meta.json`. If they differ, notify the
  * agent so it can decide when to reindex.

gitnexus-web/package.json

@@ -33,7 +33,7 @@
     "graphology-layout-noverlap": "^0.4.2",
     "isomorphic-git": "^1.36.1",
     "jszip": "^3.10.1",
-    "kuzu-wasm": "^0.11.1",
+    "@ladybugdb/wasm-core": "^0.15.1",
     "langchain": "^1.2.10",
     "lru-cache": "^11.2.4",
     "lucide-react": "^0.562.0",

gitnexus-web/src/components/EmbeddingStatus.tsx

@@ -83,7 +83,7 @@ export const EmbeddingStatus = () => {
             <button
               onClick={handleTestArrayParams}
               className="flex items-center gap-1 px-2 py-1.5 bg-surface border border-border-subtle rounded-lg text-xs text-text-muted hover:bg-hover hover:text-text-secondary transition-all"
-              title="Test if KuzuDB supports array params"
+              title="Test if LadybugDB supports array params"
             >
               <FlaskConical className="w-3 h-3" />
               {testResult || 'Test'}

gitnexus-web/src/core/embeddings/embedder.ts

@@ -275,7 +275,7 @@ export const embedBatch = async (texts: string[]): Promise<Float32Array[]> => {
 };
 
 /**
- * Convert Float32Array to regular number array (for KuzuDB storage)
+ * Convert Float32Array to regular number array (for LadybugDB storage)
  */
 export const embeddingToArray = (embedding: Float32Array): number[] => {
   return Array.from(embedding);